How do overlapping genes impact GEDmatch results?

If genetic genealogy wasn’t complicated enough, add overlapping genes into the mix, and you’re in for a world of confusion. You may struggle to determine your relationship with an unknown relative and shockingly discover a genetic match much different than what you previously thought with a known relative. GEDmatch has a tool to help you evaluate and sort out areas of DNA overlaps.

What are the principles behind overlapping genes?

When DNA companies test your DNA, they look at somewhere between 500,000 and 900,000 individual units of DNA (SNPs) of 3 billion. Each genetic genealogy company selects which locations they want to examine. Some companies choose the same area, and this is called coverage overlap.

GEDMatch Overlap: When DNA testing companies look at the same SNP

For instance, FamilyTreeDNA might overlap with 23andMe in about 200,000 of those locations. There fore, you may discover:

23andMe might have 300,000 SNPs that are different from FamilyTreeDNA

FamilyTreeDNA might have 300,000 SNPs that are different from 23andMe

To generate a DNA match, you have to match a certain number of centimorgans and a minimum number of SNPs at the locations tested. As such, the amount of overlap gene segments tested becomes essential.

While both 23andMe and FamilyTreeDNA may each test about 500,000 locations, it’s only the overlap locations that GEDMatch can examine when comparing kits from different companies.

Smaller segments of shared DNA may not appear on GEDMatch Match Lists.

As you shared smaller and smaller segments with another DNA test taker, there are fewer and fewer SNPs or overlapping genes. At some point, you may not have enough SNPs to meet the search threshold on GEDmatch. Therefore, you may not see a genetic match due to the lack of overlapping genes testing between DNA testing companies.

In the following chart, you can see how each DNA testing company tests the SNPs and view where the overlapping gene segments occur.

This chart only displays ten SNPs out of the 700,000 for demonstration purposes.

The left column defines the chip version each of the four genetic genealogy testing companies (AncestryDNA, 23andMe, MyHeritage DNA, and FamilyTreeDNA). Recognize that each time they change the chip version, these companies change which of those SNPs to include in their test.

If we look at Family TreeDNA in comparison to the AncestryDNA test, we see that FamilyTreeDNA tests on 2, 3, 4, 7, 8, and 10. The overlap with Ancestry is only 2, 3, and 10. The gaps represent a lack of data for GEDmatch to compare.

When the gaps become wide enough, you might begin losing matches on GEDmatch because the tools can not compare DNA from two different testing companies in those locations.

When comparing different chip versions within one company (such as Ancestry Version 1 and Ancestry Version 2), match results may no longer appear even though two kits used the same company.

How much DNA overlap exists between the different genetic genealogy testing companies?

The ISOGG website has an Autosomal SNP comparison chart that displays how much overlap there is between the tests. In most cases, the overlapping gene segments are about a couple hundred thousand or more SNPs.

The GEDmatch overlap is a little bit different, however. Based on the tests that I’ve taken with all the different companies, I created this overlapping SNPs table.

Family History Fanatics Autosomal SNP comparison chart

This GEDmatch database comparison chart differents from the overlapping genes chart on the ISOGG website. Why is this?

First, GEDmatch doesn’t look at every single SNP tested. GEDmatch started back in 2010. At that time, only FamilyTreeDNA and 23andMe offered DNA tests. 23andMe had their Version 3 chip testing just over 900,000 SNPs. Based on the overlap, GEDmatch is examining the vast majority of those SNP segments (almost 850,000).

With the FamilyTreeDNA chip, they tested about 700,000 SNPs. GEDmatch examines the majority of those (620,000 locations). Most of those SNPs overlap with ones from 23andMe. There are only a few thousand of the FamilyTreeDNA SNPs extra that GEDmatch added in.

Save this pin to Pinterest to remember this GEDmatch principle.

Why didn’t GEDmatch use the entire group of 23andMe and FamilyTreeDNA SNPs?

I don’t know, but GEDmatch still uses the majority of them.

As time went on, 23andMe changed their chips. AncestryDNA a began DNA testing changed their chip along the way. MyHeritage DNA started offering DNA testing (and uses the FamilyTreeDNA chip. Finally, LivingDNA came on the market, and users began transferring those kits to GEDmatch.

Because of the way that GEDmatch is storing their data, GEDmatch possibly didn’t want to expand the overall SNP count that they reviewed. If they did, they might invalidate some of the past results. Regardless, GEDmatch has continued to examine the original 870,000 SNPs locations.

In short, GEDmatch reviews a specific selection of SNPs based primarily on the 23andMe Version 3 chip and the original FamilyTreeDNA chip.

When you compare a 23andMe Version 3 test, a FamilyTreeDNA test, or a MyHeritage DNA test, then you are going to get the best matching results.

DNA matches from the AncestryDNA chip still cover about 400,000 of the SNPs common between the 23andMe and FamilyTreeDNA tests. When you attempt to compare the newer 23andMe chips and the Living DNA chip, you will have fewer segments of DNA compared on GEDmatch. As such, the lack of overlapping gene segments adversely affects your results on GEDmatch.

Learn More about Overlapping Genes:

I explain more about overlapping gene segments in this video and how it impacts your genetic genealogy research. Be sure to watch the video below.

The key point is, if you’re dealing with just one match, make sure you’re paying attention to whether or not you have significant overlap. You’ll ensure you are viewing all of your DNA matches from the various testing companies.

One Comment

Carol Sanders

Hi, my friend recently tested on ancestry, his dna ethnicity came back 100% hong kong but his matches are mostly pink overlap with only a handful not pink. He is adopted through family which he is unsure about as a television company have approached him to say they have found a match to a half sister in china (not sure how they got hold of his match results) . What could he do to try and gain better results, would it increase his chances by testing elsewhere ? or would this probably come back similar. Thanks for you time

Meet Devon Noel, Caleb, and Andy Lee. We help beginning and intermediate level genealogists understand DNA, climb their family trees, and write their ancestors' stories along the way. If family history isn't fun, you're doing it wrong.